• This record comes from PubMed

Structural Analysis of Strigolactone-Related Gene Products

Language English Country United States Media print

Document type Journal Article, Research Support, Non-U.S. Gov't

Structural knowledge of biological macromolecules is essential for understanding their function and for modifying that function by engineering. Protein crystallography is a powerful method for elucidating molecular structures of proteins, but it is essential that the investigator has a basic knowledge of good practices and of the major pitfalls in the technique. Here we describe issues specific for the case of structural studies of strigolactone (SL) receptor structure and function, and in particular the difficulties associated with capturing complexes of SL receptors with the SL hormone ligand in the crystal.

See more in PubMed

Umehara M, Hanada A, Yoshida S, Akiyama K, Arite T, Takeda-Kamiya N et al (2008) Inhibition of shoot branching by new terpenoid plant hormones. Nature 455:195–200 PubMed DOI

Gomez-Roídan Pagès V, Fermas S, Brewer PB, Puech-Pages V, Dun EA, Pillot J-P et al (2008) Strigolactone inhibition of shoot branching. Nature 455:189–194

Waters MT, Gutjahr C, Bennett T, Nelson DC (2017) Strigolactone signaling and evolution. Annu Rev Plant Biol 68:291–322 PubMed DOI

Bennett T, Leyser O (2014) Strigolactone signalling: standing on the shoulders of DWARFs. Curr Opin Plant Biol 22:7–13 PubMed DOI

Bythell-Douglas R, Waters MT, Scaffidi A, Flematti GR, Smith SM, Bond CS (2013) The structure of the karrikin-insensitive protein (KAI2) in Arabidopsis thaliana. PLoS One 8:e54758 PubMed DOI PMC

de Saint Germain A, Clavé G, Badet-Denisot M-A, Pillot J-P, Cornu D, Le Caer J-P et al (2016) An histidine covalent receptor and butenolide complex mediates strigolactone perception. Nat Chem Biol 12:787–794 PubMed DOI PMC

de Saint Germain A, Bonhomme S, Boyer F-D, Rameau C (2013) Novel insights into strigolactone distribution and signalling. Curr Opin Plant Biol 16:583–589 PubMed DOI

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN et al (2016) Outcome of the first wwPDB/CCDC/D3R ligand validation workshop. Structure 24:502–508 PubMed DOI PMC

Pozharski E, Weichenberger CX, Rupp B (2013) Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Acta Crystallogr Sect D: Biol Crystallogr 69:150–167 DOI

Weichenberger CX, Pozharski E, Rupp B (2013) Visualizing ligand molecules in Twilight electron density. Acta Crystallogr Sect F Struct Biol Cryst Commun 69:195–200 PubMed DOI PMC

Smart OS, Horský V, Gore S, Svobodová Vareková R, Bendová V, Kleywegt GJ, Velankar S (2017) Validation of ligands in macromolecular structures determined by X-ray crystallography. Acta Crystallogr Sect D: Biol Crystallogr 74:226–236

Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. FEBS J 275:1–21 PubMed DOI

Blundell TL, Johnson LN (1976) Protein crystallography. Academic Press, New York

Stout GH, Jensen LH (1989) X-ray structure determination. A practical guide. Wiley, New York

Drenth J (1999) Principles of protein X-ray crystallography. Springer, New York DOI

Kabsch W (2010a) XDS. Acta Crystallogr Sect D: Biol Crystallogr 66:125–132 DOI

Kabsch W (2010b) Integration, scaling, space group assignment and post-refinement. Acta Crystallogr Sect D: Biol Crystallogr 66:133–144 DOI

Evans PR (2011) An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr Sect D: Biol Crystallogr 67:282–292 DOI

Evans PR, Murshudov GN (2013) How good are my data and what is the resolution? Acta Crystallogr Sect D: Biol Crystallogr 69:1204–1214 DOI

Karplus PA, Diederichs K (2012) Linking crystallographic model and data quality. Science 336:1030–1033 PubMed DOI PMC

Weiss MS (2001) Global indicators of X-ray data quality. J Appl Crystallogr 34:130–135 DOI

Brändén C-I, Jones TA (1990) Between objectivity and subjectivity. Nature 343:687–689 DOI

Kleywegt GJ, Jones TA (1995) Where freedom is given, liberties are taken. Structure 3:535–540 PubMed DOI

Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr Sect D: Biol Crystallogr 67:355–367 DOI

Bricogne G, Blanc E, Brandl M, Flensburg C, Keller P, Paciorek W et al (2017) BUSTER. Global Phasing Ltd, Cambridge

Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI et al (2019) Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr Sect D: Biol Crystallogr 75:861–877 DOI

Brünger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475 PubMed DOI

Diederichs K, Karplus PA (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4:269–275 PubMed DOI

Engh R, Huber R (1991) Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr Sect D: Biol Crystallogr 47:392–400 DOI

Ramakrishnan C, Ramachandran GN (1995) Stereo-chemical criteria for polypeptide and protein chain conformations. II. Allowed conformation for a pair of peptide units. Biophys J 5:909–933 DOI

Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491–497 PubMed DOI

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242 PubMed DOI PMC

Harding MM (2006) Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr Sect D: Biol Crystallogr 62:678–682 DOI

Zheng H, Chordia MD, Cooper DR, Chruszcz M, Müller P, Sheldrick GM, Minor W (2014) Validating metal binding sites in macromolecule structures using the CheckMyMetal web server. Nat Protoc 9:156–170 PubMed DOI

Hamiaux C, Drummond RS, Janssen BJ, Ledger SE, Cooney JM, Newcomb RD, Snowden KC (2012) DAD2 is an α/β hydrolase likely to be involved in the perception of the plant branching hormone, strigolactone. Curr Biol 22:2032–2036 PubMed DOI

Kagiyama M, Hirano Y, Mori T, Kim SY, Kyozuka J, Seto Y, Yamaguchi S, Hakoshima T (2013) Structures of D14 and D14L in the strigolactone and karrikin signaling pathways. Genes Cells 18:147–160 PubMed DOI

Zhao LH, Zhou XE, Wu ZS, Yi W, Xu Y, Li S et al (2013) Crystal structures of two phytohormone signal- transducing α/β hydrolases: karrikin-signaling KAI2 and strigolactone-signaling DWARF14. Cell Res 23:436–439 PubMed DOI PMC

Stogios PJ, Onopriyenko O, Yim V, Savchenko A (2015) Crystal structure of the strigolactone receptor ShHTL5 from Striga hermonthica. Science 350:203–207 PubMed DOI

Carlsson GH, Hasse D, Cardinale F, Prandi C, Andersson I (2018) The elusive ligand complexes of the DWARF14 strigolactone receptor. J Exp Bot 69:2345–2354 PubMed DOI PMC

Hamiaux C, Larsen L, Lee HW, Luo Z, Sharma P, Hawkins BC, Perry NB, Snowden KC (2019) Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode. Biochem J 476:1843–1856 PubMed DOI

Rupp B (2010) Scientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculum. J Appl Crystallogr 43:1242–1249 DOI

Prandi C, Occhiato EG, Tabasso S, Bonfante P, Novero M, Scarpi D, Bova ME, Miletto I (2011) New potent fluorescent analogues of strigolactones: synthesis and biological activity in parasitic weed germination and fungal branching. Eur J Org Chem 2011:3781–3793 DOI

Zhao LH, Zhou XE, Yi W, Wu Z, Liu Y, Kang Y et al (2015) Destabilization of strigolactone receptor DWARF14 by binding of ligand and E3-ligase signaling effector DWARF3. Cell Res 25:1219–1236 PubMed DOI PMC

Yao R, Ming Z, Yan L, Li S, Wang F, Ma S et al (2016) DWARF14 is a non-canonical hormone receptor for strigolactone. Nature 536:469–473 PubMed DOI

Zwanenburg B, Mwakaboko AS, Kannan C (2016) Suicidal germination for parasitic weed control. Pest Manag Sci 72:2016–2025 PubMed DOI

Waters MT (2019) Spoilt for choice: new options for inhibitors of strigolactone signaling. Mol Plant 12:21–23 PubMed DOI

Hamiaux C, Drummond RS, Luo Z, Lee HW, Sharma P, Janssen BJ, Perry NB, Denny WA, Snowden KC (2018) Inhibition of strigolactone receptors by N-phenylanthranilic acid derivatives: structural and functional insights. J Biol Chem 293:6530–6543 PubMed DOI PMC

Hameed US, Haider I, Jamil M, Kountche BA, Guo X, Zarban RA, Kim D, Al-Babili S, Arold ST (2018) Structural basis for specific inhibition of the highly sensitive ShHTL7 receptor. EMBO Rep 19:e45619

Takeuchi J, Jiang K, Hirabayashi K, Imamura Y, Wu Y, Xu Y et al (2019) Rationally designed strigolactone analogs as antagonists of the D14 receptor. Plant Cell Physiol 59:1545–1554 DOI

Nakamura H, Hirabayashi K, Miyakawa T, Kikuzato K, Hu W, Xu Y et al (2019) Triazole ureas covalently bind to strigolactone receptor and antagonize strigolactone responses. Mol Plant 12:44–58 PubMed DOI

Xu Y, Miyakawa T, Nosaki S, Nakamura A, Lyu Y, Nakamura H et al (2018) Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga. Nat Commun 9:3947–3947 PubMed DOI PMC

Find record

Citation metrics

Loading data ...

Archiving options

Loading data ...